can anybody explain why you need to manually upgrade gems?
Isn't it more logic if this is done automatically? I mean you'll always want to upgrade them, no?

No, people won't always want to upgrade gems. They might want to keep them at a lower level to keep the mana cost down, or so they can swap that gem to another character which might not have enough stats to use a leveled one, or because some of their stats come from items and if they level the gem then it's requirements will be higher than their base stats, meaning they couldn't use the leveled gem if they replaced those items with others which didn't give stats.

I am on holiday until early January, and will be slow to respond to PMs until then.